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Sample GSM580026 Query DataSets for GSM580026
Status Public on Aug 16, 2010
Title HPdLF-DS13569
Sample type RNA
Source name Normal Human Periodontal Ligament Fibroblast Cells
Organism Homo sapiens
Characteristics cell type: Normal Human Periodontal Ligament Fibroblast Cells
Biomaterial provider ScienCell;7409
Growth protocol Followed vendor recommendations for growth protocol/media
Extracted molecule total RNA
Extraction protocol At cell harvest, a subset of cells was stored at -20oC in RNALater. Total RNA from 5 X 10^6 cells were purified using Ribopure (Ambion) according to vendor recommended protocols. Total RNA quality was assessed on RNA 6000 Nano Chips (Agilent) using a Bioanalyzer (Agilent).
Label biotin
Label protocol A Whole Transcript Sense Target Labeling Assay (Affymetrix) was used to reduce the rRNA, perform in vitro transcription (IVT) and create labeled sense strand DNA for hybridization to the arrays.
Hybridization protocol Hybridizations were carried out according the manufacturer (Affymetrix) protocol
Scan protocol Affymterix Gene Chip Scanner 3000
Description X_Hs_HPdLF_E_100603_34_DS13569_W_3.CEL
Data processing Intensity files from the scanned exon arrays were analyzed at the exon level (Affymetrix ExACT 1.2.1 software). Sample data were quantile normalized with PM-GCBG background correction and PLIER (Probe Logarithmic Intensity Error) summarized
Probe group file used for analysis: HuEx-1_0-st-v2.r2.pgf
Submission date Aug 16, 2010
Last update date Apr 23, 2013
Contact name ENCODE DCC
Organization name ENCODE DCC
Street address 300 Pasteur Dr
City Stanford
State/province CA
ZIP/Postal code 94305-5120
Country USA
Platform ID GPL5188
Series (1)
GSE19090 Exon arrays of ENCODE tier 1, tier 2 and tier 3 cell types

Data table header descriptions
VALUE quantile normalized with PM-GCBG background correction and PLIER (Probe Logarithmic Intensity Error) summarized

Data table
2315101 67.00365
2315102 56.25085
2315104 89.04572
2315105 39.80379
2315107 213.0671
2315112 62.31306
2315114 53.15646
2315116 39.04171
2315118 658.7274
2315120 207.6342
2315126 12.79247
2315132 7.191434E-05
2315138 49.1424
2315140 17.87606
2315142 8.134616
2315144 11.09294
2315146 33.89876
2315148 60.98889
2315149 96.73855
2315150 62.99459

Total number of rows: 1384231

Table truncated, full table size 22737 Kbytes.

Supplementary file Size Download File type/resource
GSM580026_X_Hs_HPdLF_E_100603_34_DS13569_W_3.CEL.gz 22.2 Mb (ftp)(http) CEL
GSM580026_wgEncodeUwAffyExonArrayHpdlfSimpleSignalRep2.broadPeak.gz 20.9 Mb (ftp)(http) BROADPEAK
Raw data provided as supplementary file
Processed data included within Sample table
Processed data provided as supplementary file

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